Missing Two Years
by skye3
Summary: Chapter 3 is up! During Sydney's missing two years, Vaughn saw her. What would he do about it? Could he do something to prevent everything that happened in S3? Please read and review.
1. The Haunting

Missing Two Years  
  
Disclaimer: I WISH own Alias.  
  
A/N: Hey guys! This is my second try on Alias. Hope you'd like it and I would really appreciate your reviews. Thanks!  
  
_Italicized text represents thoughts.  
_  
Chapter 1 - The Haunting  
  
Vaughn is driving like a mad dog because he is going for late for work. His class would start in 15 minutes. Fortunately heard, over the radio, that there had been an accident on the freeway so he's taking the side streets, which is a longer but traffic free zone. He was never late in anything before, not in class as a student, not in hokey practices and not as a CIA operative. And he is not planning on starting now, as a university professor. However, except for the fact that he is about to be late for his class, he feels that today is going to be fine day. It took him a while; actually it seemed like forever, to recover from the loss of the love of his life. But he has now moved on. He has a life again, a good paying job and maybe something good happening between him and his new girlfriend, Lauren. But he doesn't know that reality is about to unfold before his eyes. Fate will yet again play with him.  
  
As he speeds through the street, crossing the intersection, it happened. She ran across the street. He turned the wheel to evade her and prevent the car from running over her. His car swerved and smashed to the light post. He hit his head. He's bleeding pretty hard but that wasn't what he was so terrified about. The woman. He was sure it was her. She looked a little different but it was her. He was sure of it. He got out of the crushed car and franticly looked around to spot her. Then all went black and he dropped to the ground.  
  
He hears beeping. He inhaled. HOSPITAL. And sure enough when he opened his eyes, there he was, lying on the hospital bed with bandages all over his head and face. He moved to sit up. He winced. Broken rib or ribs for that matter. He laid back down. Flashes of the earlier event immediately came down to him. The tires screeched. She stared at him. She looked horrified. Then she ran away. _This is not possible or is it? C'mon Mike, there's no such thing as people coming back to life. But there's no such thing as ghosts either, or is there? This is all very mind-boggling. Maybe this is just a dream. But it sure a hell didn't feel like one._ His train of thought was broken when the door opened. He opened his eyes. _Yep, this is definitely not a dream. My dreams never include Weiss, not for the wrong reasons or anything._  
  
"Hey man! Good. You're awake already. How are you feeling?" Weiss sat on the chair near the bed. "What happened? You weren't drinking again, were you?"  
  
Vaughn shook his head lightly. "Weiss I saw her." Weiss gave him a confused look. "Look," he continued, "I know it sounds crazy but I swear to God I saw her Eric. I saw Sydney. She's alive."  
  
Weiss just stared at him with a blank expression on his face. Then he stood up slowly, nodding his head, "OK Mike," he approached the bed and gave his best friend a pat on the shoulder, "I think you should get some rest first. Maybe you banged your head really hard this time. I'll talk to you later, OK?" Then Weiss left immediately, not allowing him to explain any further.  
  
TBC....  
  
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So what you guys think? This is just an intro, so that you'll have an idea on the story line. The next chapter, Set Up, is on the way. So please tell me what you guys think. 


	2. Set Up

Missing Two Years

A/N: Alright, here's chapter two. Just to be clear, Vaughn and Lauren are not yet married here. They've just been dating for some time. Please write your views and thanks very much for those who did. Good day to all!

Chapter 2 – Set Up

"Eric, how is he? Is he alright?" Lauren asked when he saw Weiss in the hallway of the hospital.

"Uh...yeah Lauren, he's totally fine. Other than a slight concussion and 2 broken ribs, he's fine." He smiled brightly. They both know that Vaughn has been through worse than this. "You could go in now, he's awake, but I wouldn't believe everything he would say yet," he joked. Lauren smiled at him and headed to Vaughn's room.

"Hey, how are you feeling?" Lauren asked approaching Vaughn's bed. "I'm OK," he smiled at her. She leaned in to put a kiss on his cheek. But Lauren was the last person on his mind right now. He was too confused and bothered by what he saw but at the same time he was sure of it and he will stop at nothing until he can prove it. _Was it really her? And what was she doing? Why did she seem so terrified? And who was she running from? _

"Michael, I'll let you get some rest now. The doctor said that you can go home tomorrow, I'll pick you up then?" Lauren asked when she noticed Vaughn's lack of responsiveness to the fact that she's here visiting him. "No that's alright, I already asked Weiss to pick me up, thanks." And with that Lauren left after placing a kiss on his cheek one more time.

Vaughn closed his eyes. He was feeling very tired and his head hurt. And minutes later he was asleep. But even in his dream he saw her, repeatedly. It started from the day she "died". Her apartment burning. The DNA matches. He spread her ashes to the ocean. Jack Bristow wept. His dark days after her death. Then flashes and blurred images of her running across the street. His dream was like a slow motion of what had happened. She saw him too. She even looked shocked when she saw him. He woke up then, a thousand questions ran through his mind. _Why?_

--Next Morning--

"Mike, what are you doing? The nurse called me. She told me that you're being difficult, wanting to leave without anybody picking you up. She's worried that you might get dizzy or something along the way." Weiss said as her suddenly entered the room. "Where's Lauren? I thought she'd pick you up?" He questioned again when Vaughn didn't answer him the first time.

"I'm going home Weiss and no, I did not ask Lauren to pick me up." He said smugly, collecting his things and getting ready to leave the room. "And then I'm going to the university. I'm gonna quit my job."

"What!? Why? Do you know what you're saying? Maybe you shouldn't be going home yet."

"I saw her Weiss. She's alive and I'm going to find her."

"Mike, listen to yourself. I thought you got past this already? The DNA was a match! We already tried looking for her. It's time to accept reality buddy. I don't like it at all but it's just the way it has to be. Jack's the only one living a dream now."

"Damn it! I know that!" Vaughn was getting furious. "Just leave me alone! I'm not crazy if that's what you're thinking. I know what I saw. And maybe that's why Jack didn't want to give up -- because he knew that she's still alive. I saw Sydney Weiss, and I'm going to find her."

Weiss is getting frustrated. "Okay, tell me how you're gonna find her. You're not with the agency anymore. Where are you gonna start?" Vaughn just looked away. He didn't know how he would find her. He didn't even know IF he's ever gonna find her. The rational man that he is, of course he knew that maybe what he saw was just a hallucination or maybe he's just making a mistake. He was part of the search team for Sydney. Every intel that they got lad to a dead end. And when the CIA stopped the search, he looked for her all over the world by himself but he found nothing. Not a single trace of her. But there is also a chance that she's still alive. After all that they've seen in the job, the works of Milo Rambaldi, nothing is surprising anymore. "Okay, well then at least let me help you." Weiss said after a while. Vaughn gave him a look. "If Sydney is alive then she can be found, there's no reason otherwise, and I'm going to help you," Weiss said. "Thanks, Weiss." Weiss nodded in response. "But first you have to let me drive you to your house." And they both laughed at that.

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Vaughn was looking into the files once again, trying to find out if he had missed something before. However he found nothing. Then the doorbell rang. He got up and opened the door. _It's gotta be Lauren. _Or so he thought. "Jack...!"

"You saw her. I knew she's alive." He said, immediately getting into business and letting himself in. "Weiss told me. I have been gathering some intel and there's this new group calling themselves The Covenant that's crazy about the works of Rambaldi. I think they might be responsible for Sydney's disappearance considering that she is in Rambaldi's journal. I think they have Sydney."

"Why do you say that?"

"When Weiss told me that you saw Sydney, I looked into it. And I found out that about two blocks from the point where you saw her, an antique store was robbed. "

"Are you saying that she's working for The Covenant?" Vaughn could not believe that Sydney would do anything for some group that would stage her death and take her away from her life.

"Yes." Jack answered plainly. "But knowing Sydney, she might have been brainwashed or forced into doing it." Vaughn then nodded in agreement. Then he said, "I think I know how we could get Sydney out to the open again and lure her to us. And get her back and prove to everybody that she's alive." "Okay, what is it?" Jack replied cooperatively. "Remember what Sydney did before when we wanted to get Khasinau?" Jack nodded. "We'll do the same. If we could get The Covenant to believe that there will be an exchange of some Rambaldi artifact in a particular place, then maybe they'll send Sydney to intercept the trade, like we would do." He added as a matter-of-factly.

"Okay, I think that might work. But we need Weiss to operate inside the CIA to get the intel out. You know how the NSC has been on my back. I can't risk my freedom, not now that we're very close to getting Sydney back." Then a thought struck Vaughn, "Jack, what if I made a mistake? What if I didn't really see Sydney? What if I was just hallucinating?"

"You weren't Agent Vaughn," came Jack's strong and straight-faced reply. Then he left. Tomorrow they would carry out their plan.

TBC.....

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I'm sorry if this one's boring. I promise I'll try to make the next one interesting. Thanks for reading and please let me know what you think.


	3. Benevolent Conspiracy

Missing Two Years

A/N: Hi! Sorry it took me a long time to getchapter three done. I got busy with homeworks and projects. You know, school stuff. Also, I had a little difficulty thinking about what should happen next and how it should happen. Never the less, here's chapter three. Hope you like it.

Chapter 3 – Benevolent Conspiracy

"Weiss, Jack and I talked. We have a plan and we need you to pull some strings in the CIA."

"Okay, I'll meet you at the safe house." Weiss hung up the phone, grabbed some files and headed out towards the basement parking lot.

"Eric! Wait a second!" It was Lauren. "Have you been able to talk to Michael? I've been trying to call him but all I get is the answering machine. He's not answering his cell phone either. Where is he? Is he okay?" She asked worriedly. "He's fine Lauren. Maybe he's just busy with checking the papers of his students, that's all." He smiled at her, and then continued, "Now, if you'll excuse me, I have to go meet somebody." "Okay, thanks Weiss." Then she walked to her desk. She thought for a while. After sometime she picked up the phone and dialed the number for the UCLA. "Hello, this is Lauren Reed, may I please talk to Michael Vaughn?"

"I'm sorry Miss Reed, but Mr. Vaughn have already resigned yesterday," came the reply of the lady on the other side. "Oh, okay then, thank you," Lauren hung up. Confusion and suspicion evident on her face. _Why didn't Weiss tell me? What's going on? Something's up, I know it._ Then she stood up, got her bag and left.

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Vaughn arrived at the safe house first. He slowly walked through the familiar dark hallway. It felt like a long time since he had been here. This place brings back so many memories. Memories of Sydney. This was their meeting place. This is where they would make plans to take down SD-6, talk about missions or for some other cases, cases that he loved the most, they'll just sit here chatting just about anything outside the spy world. This is where they shared their worries and pains to each other. This is where they would sometimes argue with each other. This is where they shared hugs and intimate kisses. This was also the place where he hid himself from the world when she "died." He had spent countless days in the darkness of the safe house drinking, thinking of her, talking to her.

His thoughts were cut short when he heard the clattering of the railings.

"Hey man, what's up?" Sure enough it was Weiss.

"Weiss," Vaughn approached his best friend, "thanks for coming."

"No problem, here's everything on Sydney." He handed the folders to Vaughn.

What do you need that for anyway?"

"Thanks. I just thought that maybe there's something here that may help us know what happened to Sydney that we did not notice before." Vaughn explained.

"Okay, so what's the plan?"

"Jack believes that Sydney is being held by The Covenant and that they had been using her, sending her to missions," Vaughn started intently.

"Wait, did you say The Covenant? That's the group that the CIA has been trailing for some time now." Weiss added.

"Yes, that's it. So here's the plan. We'll leak a bogus intel that says that there would be transport of a Rambaldi artifact tomorrow night at the harbor, ship number 0905. When The Covenant picks up the intel, chances are they would send Sydney to intercept the package. And we'll be there, waiting." Vaughn finished with determination.

"Okay, so I'll just have to send the intel from the CIA right?" Weiss clarified. "Yeah, and we'll also need you at the pier tomorrow." Vaughn replied. The Weiss' phone rang. "Weiss here…Okay, I'll be right there." Vaughn nodded and tapped Weiss' shoulder as he started walking to open the gate.

"Hey Mike," he turned before he left, "Lauren's been asking about you. You should talk to her." Vaughn nodded. Vaughn stayed there for a little bit longer, making sure that everything was planed clearly.

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"I think they're trying to look for Bristow again," Lauren reported to whoever was on the other side of the phone. "I suggest that you don't send her on any missions for a week or two. Okay…I'm meeting with Lindsay now," She paused to open her window to show her ID to the guard. "I have to go." She hung up and parked her car.

"Ms. Reed, Director Lindsay is waiting for you in his office." The guard in the parking area approached her as she was getting out of her car. "Okay. Thanks," She smiled.

Lauren entered Lindsay's office after a while. "So, Ms. Reed how's everything going at the CIA?" Lindsay inquired. "It's been okay," she paused and thought whether or not she should tell Lindsay about her suspicion. "Alright, now I want you to know that…."

"Except for one thing," Lauren interrupted.

"What is it?"

"I think that, Jack Bristow, Eric Weiss and maybe, just maybe, Michael Vaughn are looking for Sydney Bristow again."

"Michael Vaughn? The former handler of Bristow? I thought he's already out of the CIA?" Lauren nodded. "Are you sure? How do you know?" Lindsay questioned.

"I'm not sure but I have noticed that Weiss has been talking on the phone with Michael and just this morning I found out that he pulled Sydney Bristow's file and photo copied everything."

"I see, that's not right," Lindsay said sternly, "that search operation has been ordered to stop last year." Then he paused, thought for a while then said, "Okay, Ms. Reed, you may go now. I know that you and Michael Vaughn are in a relationship but you did not let that interfere with your duties to the NSC. Keep up the good work." With that Lauren left after saying thank you. Lindsay picked up the phone, "Director Dixon, I received a report that some of your agents together with a certain former agent are conduction unauthorized operations searching for Sydney Bristow, a person that has long been dead by now! You better put a cork on this or I'll be the one to report this on the higher level," he threatened and hung up.

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Weiss parked in Vaughn's drive way. He prepared himself before getting out of the car. Vaughn wouldn't be happy at all when he hears about this. He sighed and walked to ring the bell.

"Weiss, good. You're here." Vaughn said, "I have reviewed everything and we're good to go." Vaughn finished confidently. "Have you sent the intel to the Covenant?"

"Yes, but we have a problem." Weiss stated making Vaughn's forehead crease.

"What is it?"

"We have been suspended, Jack and I. Director Dixon received a call from the NSC reporting what we are trying to do. I don't know how they found out but they did. I mean, we both know that we're not supposed to be doing this." Weiss finished sitting down on the sofa.

"What? Are you serious?" Vaughn asked furiously.

Weiss nodded in response. "Director Dixon called us in, he said that he understood us for not giving up the search for Sydney but, as we all know, it was already been ordered to stop, we disobeyed, so he had no choice but to suspend us. He ordered us not to carry on whatever plan we have or we'll lose our job. I'm lucky because I'm just being suspended, I heard Jack is being investigated."

"That son of a bitch! The fact that he suspended you instead of helping us shows that he does not understand at all! He doesn't care! All he cares about now is keeping his position!" Vaughn stormed furiously.

"C'mon Mike, don't say that. You know how Dixon cares about Sydney. Of course he also wants to find Sydney but if we all get dismissed then it would be much harder for us to find her."

Vaughn sighed and sat beside Weiss on the couch. Then the phone rang but neither of them was in the mood to answer it. So the answering machine went off. "Hi. Michael Vaughn here. Leave a message after the beep."

"Vaughn. It's me, Dixon. Weiss probably told you already that I suspended him and Jack. I had to. I had to put up a show to whoever reported them. And I want you to know, that whatever you have planed, count me in. You know where to find me." Then he hung up. Weiss smiled at Vaughn. "What did I tell you?"

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That night they carried out their plan. They were all there geared up just in case that they have to fight off a number of people to get Sydney. Vaughn, Weiss, Jack and Dixon, they were all there but Sydney wasn't. She did not show up. There were two men who showed up instead, they checked the ship out then left. They waited till sunrise and by then they were pretty sure that she wouldn't show. So they left. Everyone went to their designated places. Weiss went home. He was suspended. Jack drove away to nobody knows where. Dixon went to the CIA. Vaughn stayed at the harbor. He just sat there and before he knew it the sun was already setting. He got up and drove to the ice rink. He needed to feel the coolness of the ice. That always helps take the frustration and sadness away. He did that when his father passed away. He skated hard, as fast as he could until he got tired. He laid on the ice with his eyes closed. He thought about a million things. He tried to think of a reason why she didn't show up. _Maybe the Covenant discovered that the intel was bogus. Maybe luck was just not on their side that the covenant sent those two men to intercept the artifact instead of sending her._ _Or maybe…_He stopped. He did not want to entertain that thought. But it kept ringing on his head. _Maybe she's really gone. Maybe she really did die._ "No!" He hit the ice. Blood oozing out of his knuckles but he didn't care. After some time, when he got to his senses and realized that he's already shivering from the cold, he stood up and went home.

Vaughn parked his car. He sighed heavily and got out of his car. He fondled on his keys. It was too dark and his hand hurt and he was tired. He cursed when he dropped the keys. He picked it up located the right key and shoved it to the knob. Angrily, he kicked the door open and slammed it shut as he went inside. He sunk to the floor, leaning on the door. Then he saw something moved towards him. Instinctively, he reached for his gun but it wasn't there, he left it in the car.

"Who's that?" he stood up immediately and motioned to turn on the lights.

"Stop! It's me. Don't turn on the lights!"

Vaughn froze.

TBC….

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So, what do you think? I know, it's pretty obvious who the person is. But hopefully you liked it. Thanks for reading and thanks also to those who wrote their comments and reviews. You guys keep me determined to finish this story. Keep the reviews coming. I'd love to know your thoughts. I'll try to begin and finish with the next chappie as soon as I can. Until then….Happy Holidays!


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